Without seeing your code it's hard to say exactly what the problem is, but I have had this issue in the past when positioning items using a static value. Essentially, the height changes but the static position doesn't which leaves your element offset a bit. If this is your issue you can fix it like this:
HTML
<div class="flex-nav-container">
<ul class="flex-direction-nav">
<li><a class="flex-prev">Previous</a></li>
<li><a class="flex-next">Next</a></li>
</ul>
</div>
CSS
.flex-nav-container { position: relative; height: 300px; //or whatever }
.flex-direction-nav a { position: absolute; height:30px; top: 50%; margin-top: -15px; }
.flex-prev { left: 0; }
.flex-next { right: 0; }
That will center the top of the arrow element to the 50% spot on the slider's height. By adding the negative margin as half of the height of the arrow you are essentially centering the arrow vertically regardless of the height of the slider.
JSFiddle Demo
Try changing the height of .slider
to see what is actually happening. I added some color to show the elements.